Predicting Octanol–Water Partition Coefficients: Are Quantum Mechanical Implicit Solvent Models Better than Empirical Fragment-Based Methods?

2019 ◽  
Vol 123 (31) ◽  
pp. 6810-6822 ◽  
Author(s):  
Varun Kundi ◽  
Junming Ho
Keyword(s):  
Partition Coefficients ◽  
Quantum Mechanical ◽  
Implicit Solvent ◽  
Solvent Models ◽  
Implicit Solvent Models ◽  
Better Than

scholarly journals The validation of quantum chemical lipophilicity prediction of alcohols

2016 ◽  
Vol 9 (2) ◽  
pp. 89-94 ◽  
Author(s):  
Martin Michalík ◽  
Vladimír Lukeš
Keyword(s):  
Linear Correlation ◽  
Quantum Chemical ◽  
Partition Coefficients ◽  
The Other ◽  
Basis Set ◽  
Implicit Solvent ◽  
Solvent Models ◽  
Lipophilicity Prediction ◽  
Triple Zeta ◽  
Implicit Solvent Models

AbstractThe validation of octanol-water partition coefficients (logP) quantum chemical calculations is presented for 27 alkane alcohols. The chemical accuracy of predicted logPvalues was estimated for six DFT functionals (B3LYP, PBE0, M06-2X, ωB97X-D, B97-D3, M11) and three implicit solvent models. Triple-zeta basis set 6-311++G(d,p) was employed. The best linear correlation with the experimental logPvalues was achieved for the B3LYP and B97-D3 functionals combined with the SMD model. On the other hand, no linearity was found when IEF-PCM or C-PCM implicit models were employed.

scholarly journals Predicting Octanol–Water Partition Coefficients of Fluorinated Drug-Like Molecules: A Combined Experimental and Theoretical Study

2020 ◽  
Vol 73 (8) ◽  
pp. 677
Author(s):  
Ying Min Wu ◽  
Yuvixza Lizarme Salas ◽  
Yun Cheuk Leung ◽  
Luke Hunter ◽  
Junming Ho
Keyword(s):  
Partition Coefficients ◽  
Theoretical Study ◽  
Log P ◽  
Implicit Solvent ◽  
Mean Absolute Deviation ◽  
Empirical Methods ◽  
Absolute Deviation ◽  
Solvent Models ◽  
Solvent Model ◽  
Implicit Solvent Models

In this paper, a dataset of 11 fluorinated compounds containing a variety of functional groups (amides, esters, indoles, and ethers) as well as mono, gem-difluoro, erythro-difluoro, and threo-difluoro patterns were synthesised and their octanol–water partition coefficients (log P) were measured using a shake-flask method. The resulting data was used to assess the performance of several popular empirical fragment-based methods as well as quantum chemical implicit solvent models (SMD and SM12). Overall, the empirical miLOGP, ALOGPS, and ALOGP methods performed the best with a mean absolute deviation (MAD) of ~0.25 log units, while the best performing implicit solvent model SMD has a slightly higher MAD of 0.36 log units. Based on the present work and previous studies, the miLOGP and ALOGP empirical methods are recommended for fast and moderately accurate prediction of log P for neutral organic solutes.

Generalized Born implicit solvent models for small molecule hydration free energies

2017 ◽  
Vol 19 (2) ◽  
pp. 1677-1685 ◽  
Author(s):  
Martin Brieg ◽  
Julia Setzler ◽  
Steffen Albert ◽  
Wolfgang Wenzel
Keyword(s):  
Free Energy ◽  
Small Molecules ◽  
Implicit Solvent ◽  
Free Energies ◽  
Hydration Free Energy ◽  
Energy Estimation ◽  
Generalized Born ◽  
Solvent Models ◽  
Molecular Force ◽  
Implicit Solvent Models

Hydration free energy estimation of small molecules from all-atom simulations was widely investigated in recent years, as it provides an essential test of molecular force fields and our understanding of solvation effects.

First-Shell Solvation of Ion Pairs:  Correction of Systematic Errors in Implicit Solvent Models†

2004 ◽  
Vol 108 (21) ◽  
pp. 6643-6654 ◽  
Author(s):  
Zhiyun Yu ◽  
Matthew P. Jacobson ◽  
Julia Josovitz ◽  
Chaya S. Rapp ◽  
Richard A. Friesner
Keyword(s):  
Ion Pairs ◽  
Systematic Errors ◽  
Implicit Solvent ◽  
Solvent Models ◽  
Implicit Solvent Models

scholarly journals Computational studies of peptide-induced membrane pore formation

2017 ◽  
Vol 372 (1726) ◽  
pp. 20160219 ◽  
Author(s):  
Richard Lipkin ◽  
Themis Lazaridis
Keyword(s):  
Pore Formation ◽  
Coarse Grained ◽  
Future Research ◽  
Implicit Solvent ◽  
Computational Studies ◽  
Membrane Pore ◽  
Membrane Pores ◽  
Solvent Models ◽  
Future Research Directions ◽  
Implicit Solvent Models

A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs. This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.

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